This application update includes an improved and optimized energy function developed mainly by Frank DiMaio and Hahnbeom Park, and others which improves on all scientific benchmarks. This is an exciting development which we would like to push out and test further. This update also includes new protocols since it uses current Rosetta source. At this point I have included a 64bit linux version but did not compile with SSE optimizations as it will require more testing. I did turn on SSE for the windows app.

For the 3.62 update, I reverted the windows application back to the 32bit non-sse build, and also reverted the linux application to the 32bit build (for the 64bit apps). There was a significant fraction of errors which prompted the change. We will do another update soon related to the "Option matching -relax:cyclic_peptide not found in command line top-level context" errors.

For the 3.62 update, I reverted the windows application back to the 32bit non-sse build, and also reverted the linux application to the 32bit build (for the 64bit apps). There was a significant fraction of errors which prompted the change. We will do another update soon related to the "Option matching -relax:cyclic_peptide not found in command line top-level context" errors.

Errors in addition to the "Option matching -relax:cyclic_peptide not found in command line top-level context" ??

For the 3.62 update, I reverted the windows application back to the 32bit non-sse build, and also reverted the linux application to the 32bit build (for the 64bit apps). There was a significant fraction of errors which prompted the change. We will do another update soon related to the "Option matching -relax:cyclic_peptide not found in command line top-level context" errors.

on Linux-64 got some

ERROR: Option matching -abinitio:cyclic_peptide not found in command line top-level context

where the error string is a little bit different to yours
eg this workunit

As a general software engineering/debugging principal, I would not recommend mixing cpu optimizations and new code in the same build. If a WU fails, what caused it to fail? The new code or one of the optimizations?

Instead, make as many branches as you need off the branch of the latest stable build in production, and start testing the optimizations one at a time. Test against work units that have already been run successfully on the stable code base without the optimizations.

By following this procedure, you will only be testing one change at a time, for instance enabling SSE or SSE2. So, debugging will be far more straightforward in the case of any WU failures.

The protocol code for the majority of jobs (and all the test jobs) hasn't changed. BUT, for this cyclic peptide error, the developer did not check his code into the main source repo as he should have long ago. In an effort to save time a while ago, we incorporated his code before he checked it in under the understanding he would check it in soon after, which he didn't. But on a positive note, he is busy trying to make and characterize his cyclic peptide designs now.

The protocol code for the majority of jobs (and all the test jobs) hasn't changed. BUT, for this cyclic peptide error, the developer did not check his code into the main source repo as he should have long ago. In an effort to save time a while ago, we incorporated his code before he checked it in under the understanding he would check it in soon after, which he didn't. But on a positive note, he is busy trying to make and characterize his cyclic peptide designs now.

What kind of errors was the SSE extension giving then?

Remember that improving performance directly improves scientific benchmarks. There is lots of compute power in RALPH to bug-out any problems that come from using SSE/SSE2 (thought technically there shouldn't be any, since 99% of users are using SSE2 capable CPUs).

Thanks, David.
So, to be clear, would the following release notes reflect the version of 3.62 that went to production?

Improvements:
- Improved and optimized energy function developed mainly by Frank DiMaio and Hahnbeom Park and others which improves on all scientific benchmarks
- This update also includes new protocols since it uses current Rosetta source (Ed - What are the *new* protocols that were not in 3.59?)

Not Changed:
- reverted the windows application back to the 32bit non-sse build
- reverted the linux application to the 32bit build (for the 64bit apps), non-sse build